After a night of heavy drinking at the Globe and Anchor, a watering hole for enlisted US marines in Okinawa, Japan, a female service member awoke in her barracks room as a man was raping her, she reported. She tried repeatedly to push him off. But wavering in and out of consciousness, she couldn't stop him.

A rape investigation, backed up by DNA evidence, ended with the accused pleading guilty to a lesser charge: wrongfully engaging in sexual activity in the barracks. He was reduced in rank and confined to his base for 30 days. He received no prison time.

Fast forward a year. A drunk male service member was helped into bed by a male marine with whom he had spent the day. The marine then performed oral sex on the victim "for approximately 20 minutes against his will", records show. The accused insisted the sex was consensual, but he was court martialled, sentenced to six years in prison, busted to E-1, the military's lowest rank, and dishonourably discharged.

The two cases, both adjudicated by the 1st Marine Aircraft Wing, are among more than 1,000 reports of sex crimes involving US military personnel based in Japan between 2005 and early 2013. Obtained through the Freedom of Information Act, the records show a pattern of random and inconsistent judgments in the world of military justice.

The news comes as Congress is considering stripping senior officers of their authority to decide if serious crimes should be tried. The Associated Press found that the handling of allegations in Japan - home to the largest population of overseas American military personnel - verged on the chaotic, with seemingly strong cases often reduced to lesser charges. In two rape cases, commanders overruled recommendations to court martial and dropped the charges instead.

Even when military authorities agreed that a crime had been committed, the suspect was unlikely to serve time.

Nearly two-thirds of 244 service members whose punishments were detailed in the records were not incarcerated.

Instead they were fined, demoted, restricted to base or removed from the military. In more than 30 cases, a letter of reprimand was the only punishment.

Among the other findings:

The marines were far more likely than other branches to send offenders to prison, with 53 prison sentences out of 270 cases. By contrast, of the navy's 203 cases, only 15 were sentenced to time behind bars.

Victims increasingly declined to co-operate with investigators or recanted, a sign they may have been losing confidence in the system. In 2006, the Naval Criminal Investigative Service, which handles the navy and marine corps, reported 13 such cases; in 2012, it was 28.

In one case, a woman alleged that a sailor raped her. Later, she confronted him in a recorded conversation. She accused him of pushing her down "for sex purposes", after which he apologised for hurting her "in that way".

An Article 32 hearing recommended a court martial on rape charges, but the commanding officer said no. The charges were dropped.

US Senator Kirsten Gillibrand, who leads the Senate Armed Services' personnel subcommittee, says the records are "disturbing evidence" that there are commanders who refuse to prosecute sexual assault cases.

She leads lawmakers from the Republican and Democratic parties pressing for changes in the military's legal system.

"[Military personnel] deserve unbiased, trained military prosecutors reviewing their cases, and making decisions based solely on the merits of the evidence in a transparent way," says Gillibrand.

[Military personnel] deserve unbiased prosecutors

US SENATOR KIRSTEN GILLIBRAND

Air Force Colonel Alan Metzler says the Department of Defence has been open in acknowledging that it has a problem.

Metzler, deputy director of the Defence Department's Sexual Assault Prevention and Response Office, says the changes in military law and policy made by Congress and the Pentagon are creating a culture where victims trust that their allegations will be taken seriously and perpetrators will be punished. The cases examined by the AP preceded changes that the Pentagon carried out in May, according to defence officials.

The military, Metzler says, is making progress. Sexual assault cases taken to courts martial military-wide have grown steadily, from 42 per cent in 2009 to 68 per cent in 2012, according to department figures. In 2012, of the 238 service members convicted, 74 per cent served time.

That trend is not reflected in the Japan cases. Out of 473 sexual assault allegations against sailors and marines between 2005 and 2013, just 116, or 24 per cent, ended in courts martial.

Further, the 238 convictions are a small number compared with the estimated 26,000 sex crimes that may have occurred that year across the military, according to the department's anonymous survey of military personnel. Sex crimes are vastly under-reported in both military and civilian life.

Bypassing senior officers

The Pentagon has said its commanders have been using non-judicial punishment less frequently in recent years. But the documents show that in Japan, US commanders are using that authority more often. This is especially true in the navy, where in 2012 just one case led to a court martial. In the 13 others, commanders used non-judicial penalties rather than ordering trials.

Senior officers would lose the authority to decide how to prosecute serious criminal allegations under a bill written by Gillibrand that will be debated by the Senate in the coming days. The legislation would place the prosecution authority with trial counsels with prosecutorial experience who hold the rank of colonel or above.

Senior US military leaders oppose the plan, saying it would undermine the ability of commanders to ensure discipline within their ranks.

"I don't know how we can trust our commanders to train our sons and daughters to fight … and yet not trust them to provide and establish a command climate that provides each and every soldier a safe working environment," says retired General Ann Dunwoody.

US Senator Lindsey Graham agrees. "Taking the commander out of the loop never solved any problem," says Graham. "It would dismantle the military justice system beyond sexual assaults. It would take commanders off the hook for their responsibility to fix this problem."

Our commanders must be trusted] to provide a safe environment

RETIRED GENERAL ANN DUNWOODY

Graham says victims of sexual assault have a far better chance of getting justice than do victims whose cases are handled by civilian courts.

But research by Cassia Spohn, a professor of criminology and criminal justice at Arizona State University, found that civilian courts prosecute sexual assault cases at a higher rate than the military - 50 per cent compared with 37 per cent.

Mark Russell, a psychologist who was stationed in Japan, says putting commanders in charge of deciding how to proceed with sex abuse allegations can conflict with the unit's mission.

Many of the Japan cases involved an accuser who said he or she was sexually abused while too drunk to consent, or was even unconscious. That makes it all the more difficult to determine whether a crime occurred.

"Weakness is a great fear in the military and something to be avoided," Russell says. "Therefore, women [or men] who go out drinking and are raped are often viewed as culpable for having been 'weak and vulnerable'."

Sex crimes against Okinawans have become major news stories, and added fury to protests against the US military's presence on the island. The documents show that US service members who commit sexual assaults are most likely to abuse their own comrades.

More than 35 NCIS case summaries describe investigations that appeared to indicate a sex crime, but were resolved using lesser charges or simply dropped with little or no explanation.

Lenient punishment

Airman Tina Wilson's name is redacted from the report, but she spoke up a day after she went to the health clinic at Naval Air Facility Atsugi, a US base southwest of Tokyo, to have a dressing changed following surgery.

In Wilson's statement to NCIS and other records, the doctor, Lieutenant Commander Anthony Velasquez, looked at the wound as a corpsman took care of the dressing. Then Velasquez said he was going to check Wilson's lymph nodes.

He checked her neck, then went under her shirt and then slid his hand down the front of her pants and under her underwear.

Wilson pulled up her pants, and confused and shaken, headed for the door.

"I saw Dr Velasquez smile and wink at me on the way out," her statement reads. "The whole exam, he didn't wear gloves."

The NCIS document summarising the investigation prompted by Wilson's complaint shows that three other women subsequently came forward, saying Velasquez had touched them inappropriately.

But after 10 months an investigation was closed with no action. According to the document, Yokosuka Naval Hospital declined to take any action against the doctor, and the navy legal services office in Yokosuka determined the case would not be forwarded to navy officials in San Diego who oversee medical operations in Japan.

Finally in 2010, after accusations from more than two dozen women, the navy filed multiple counts of sexual misconduct and other charges against Velasquez.

Most of the charges were dropped under a plea deal. Velasquez served a week in the brig, was dismissed from the navy, lost his licence to practise medicine, and was required to register as a sex offender. Wilson, 27, left the Navy, distraught over how her case had been handled.

US commanders' role questioned in sex assault cases

The US Congress last year made several changes to the military's legal system to combat an epidemic of sexual assaults.

The defence policy bill scaled back but did not eliminate the role senior commanders play in sexual assault cases. Officers who have the power to convene courts martial were stripped of their authority to overturn guilty verdicts reached by juries. Should they decline to prosecute a case, a review must be conducted by the service's civilian secretary.

The argument for keeping commanders involved in sexual assault cases received a boost from a panel of experts, which said last month that there is no evidence that removing commanders from the process will reduce sex crimes or increase the reporting of them.

"Skippers have had this authority since the days of John Paul Jones and sexual assaults still occur," said Lory Manning, a retired navy captain and senior fellow at the Women in the Military Project. "And this is where we are." John Paul Jones was a well known naval fighter in the American war of independence.